Exemplo n.º 1
0
def multipartite_view_add(request):
    context = RequestContext(request)
    context.update(csrf(request))
    request_data = request.POST
    if not request_data:
        return render_to_response('goldenbraid_info.html',
                               {'info': "Not enougth data to add the feature"},
                                context_instance=RequestContext(request))
    multi_type = request_data['category']

    allowed_categories = PARTS_TO_ASSEMBLE.keys() + ['free']
    if multi_type is None or multi_type not in allowed_categories:
        return render_to_response('goldenbraid_info.html',
                               {'info': "Not enougth data to add the feature"},
                                context_instance=RequestContext(request))
    if multi_type == 'free':
        part_types = request_data['order'].split(':')
    else:
        part_types = [p[0] for p in PARTS_TO_ASSEMBLE[multi_type]]

    multi_data = {'Vector': request_data['Vector']}
    for part_type in part_types:
        multi_data[part_type] = request_data[part_type]

    assembled_seq = assemble_parts(multi_data, part_types)
    name = request_data['name']
    temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(assembled_seq.id),
                                    suffix='.gb')
    temp_fhand.write(assembled_seq.format('gb'))
    temp_fhand.flush()
    temp_fhand.seek(0)

    props = {'Description': [request_data['description']],
             'Reference': [request_data['reference']]}
    try:
        feature = add_feature(name=name, type_name=TU_TYPE_NAME,
                              vector=request_data['Vector'],
                              genbank=temp_fhand, props=props,
                              owner=request.user, is_public=False)

    except IntegrityError as error:
        print error
        if 'feature already in db' in str(error):
            # TODO choose a template
            return render_to_response('feature_exists.html',
                                      {},
                            context_instance=RequestContext(request))
        else:
            return HttpResponseServerError()
    except Exception as error:
        print error
        return HttpResponseServerError()
    # if everithing os fine we show the just added feature
    return redirect(feature.url)
Exemplo n.º 2
0
    def test_add_feature(self):
        'It tests the add_feature function'
        name = 'test_name'
        type_name = VECTOR_TYPE_NAME
        vector = None
        genbank = os.path.join(TEST_DATA, 'pANT1_uniq.gb')
        props = {ENZYME_IN_TYPE_NAME: ['BsaI'],
                 ENZYME_OUT_TYPE_NAME: ['BsaI']}
        try:
            add_feature(name, type_name, vector, open(genbank), props,
                        'test_user')
            self.fail()
        except RuntimeError as error:
            if 'the given user does not exist' in str(error):
                pass
            else:
                raise
        User.objects.create_user(username='******', email='*****@*****.**',
                                 password='******')
        add_feature(name, type_name, vector, open(genbank), props, 'admin')

        feat = Feature.objects.get(uniquename='pANT1_uniq')
        assert FeatureRelationship.objects.filter(object=feat).count() == 0
        assert feat.uniquename == "pANT1_uniq"
        os.remove(os.path.join(proj_settings.MEDIA_ROOT,
                               feat.genbank_file.name))

        # add relationships to feature
        # first we need to add derives from to db as it is not in the fixtures
        name = 'GB_UA_17A'
        vector = 'pDGB1_alpha1'
        type_name = TU_TYPE_NAME
        genbank = os.path.join(TEST_DATA, 'GB_UA_17A.gb')
        props = {ENZYME_IN_TYPE_NAME: ['BsaI'],
                 ENZYME_OUT_TYPE_NAME: ['BsaI']}
        # add_feature(name, type_name, vector, open(genbank), props, 'admin')
        feat = Feature.objects.get(uniquename='GB_UA_17A')
        assert FeatureRelationship.objects.filter(object=feat).count() == 2
Exemplo n.º 3
0
def crispr_view_add(request):
    context = RequestContext(request)
    context.update(csrf(request))
    request_data = request.POST
    # request_data
    seq = request_data['seq']
    category = request_data['category']
    prefix = request_data['prefix']
    suffix = request_data['suffix']
    seq_name = request_data['seq_name']
    name = request_data['name']
    if category == 'None':
        category_name = 'Other'
    else:
        category_name = CRYSPER_CATEGORIES[category][0]
    print 'seq', seq
    seq = SeqRecord(Seq(seq, DNAAlphabet()), id=seq_name, name=seq_name)
    print 'seq', seq
    temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(seq.id),
                                    suffix='.gb')
    temp_fhand.write(seq.format('gb'))
    temp_fhand.flush()
    temp_fhand.seek(0)
    props = {'Description': [request_data['description']],
             'Reference': [request_data['reference']]}
    try:
        feature = add_feature(name=name, type_name=category_name,
                              vector=None, genbank=temp_fhand, props=props,
                              owner=request.user, is_public=False,
                              prefix=prefix, suffix=suffix)

    except IntegrityError as error:
        print error
        if 'feature already in db' in str(error):
            # TODO choose a template
            return render_to_response('feature_exists.html',
                                      {},
                                      context_instance=RequestContext(request))
        else:
            return HttpResponseServerError()
    except Exception as error:
        raise
        print error
        return HttpResponseServerError(error)
    # if everithing os fine we show the just added feature
    return redirect(feature.url)
Exemplo n.º 4
0
def bipartite_view_add(request):
    context = RequestContext(request)
    context.update(csrf(request))
    request_data = request.POST
    if not request_data:
        return render_to_response('goldenbraid_info.html',
                               {'info': "Not enougth data to add the feature"},
                                context_instance=RequestContext(request))
    name = request_data['name']
    vector_name = request_data['Vector']
    used_parts = {'Vector': vector_name,
                  'part_1': request_data['part_1'],
                  'part_2': request_data['part_2']}
    seq = assemble_parts(used_parts, ['part_1', 'part_2'])
    props = {'Description': [request_data['description']],
             'Reference': [request_data['reference']]}
    temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(seq.id), suffix='.gb')
    temp_fhand.write(seq.format('gb'))
    temp_fhand.flush()
    temp_fhand.seek(0)
    try:
        feature = add_feature(name=name, type_name=MODULE_TYPE_NAME,
                              vector=vector_name, genbank=temp_fhand, props=props,
                              owner=request.user, is_public=False)

    except IntegrityError as error:
        print error
        if 'feature already in db' in str(error):
            # TODO choose a template
            return render_to_response('feature_exists.html',
                                      {},
                            context_instance=RequestContext(request))
        else:
            return HttpResponseServerError()
    except Exception as error:
        print error
        return HttpResponseServerError(error)
    # if everithing os fine we show the just added feature
    return redirect(feature.url)